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Author Topic:   A test for claimed knowledge of how macroevolution occurs
Faith 
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From: Nevada, USA
Joined: 10-06-2001


Message 121 of 785 (854858)
06-13-2019 4:45 PM
Reply to: Message 118 by Taq
06-13-2019 4:24 PM


They sequenced the genomes of the father, mother, and child to measure the de novo mutation rate. Those are mutations. You can hold the parent's DNA up to the child's DNA and see where the mutations happened. How can you say that these are not mutations when we can observe them happening in real time?

Well, but aren't you just talking about observed differences, and how do you know those differences are the result of mutations rather than the result of sexual recombination producing/selecting a new set of alleles?

Edited by Faith, : No reason given.


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Taq
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Posts: 8523
Joined: 03-06-2009


(2)
Message 122 of 785 (854859)
06-13-2019 4:48 PM


Genetic Diveristy is Consistent With Biochemistry
Just a little context for my previous posts. Here is a chart for transition and transversion substitutions:

Transition mutations are substitutions for bases that are structurally similar. Adenine and guanine have two rings while thymine and cytosine have one ring. Therefore, it is more likely for the protein that is copying DNA to substitute similar bases than dissimilar bases. Due to biochemistry, we would expect naturally caused substitution mutations to be biased towards transitions over transversions.

There is also a second major mechanism. If there is a two base sequence CG (called CpG because of the phosphate between them on the DNA backbone) then the C can be methylated by proteins in the cell nucleus. A methylated C can be deaminated into a T.

The fingerprint of naturally occurring mutations is a high rate of CpG mutations and transitions outnumbering transversions. We know this is the natural process because we understand the biochemistry and also observe these same rates in new organisms. When we see this fingerprint in a comparison of genomes it is smoking gun evidence that those differences were produced by known and observable natural processes.


  
JonF
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Posts: 6174
Joined: 06-23-2003


(2)
Message 123 of 785 (854860)
06-13-2019 4:50 PM
Reply to: Message 117 by Faith
06-13-2019 4:12 PM


"Mutation" is defined as a change in the sequence of amino acid molecules in DNA.

We get some DNA from our mother and some from our father. Any DNA we have that is different from both our mother and father is a mutation. That's by definition.

We can and do compare DNA sequences and detect mutations.

The differences between someone's DNA and both their parents, which we label as mutat, did not exist anywhere before. Not in the mother's DNA, not in the father's DNA, not anywhere. No amount of redefinition or argument can change that fact. It does not depend on assumptions or worldview.

Mother's DNA + father's DNA + mutations = your DNA. There's no other physically possible source of your DNA.


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Taq
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Posts: 8523
Joined: 03-06-2009


(1)
Message 124 of 785 (854861)
06-13-2019 4:50 PM
Reply to: Message 121 by Faith
06-13-2019 4:45 PM


Faith writes:

Well, but aren't you just talking about observed differences, and how do you know those differences are the result of mutations rather than the result of sexual recombination producing a new set of alleles?

If they were the result of recombination then the child's DNA would match one of the alleles carried by the parents. This isn't what they see. The child has a difference in its DNA not found in either parent, not in any of their alleles. This is a mutation by definition.


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PaulK
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Joined: 01-10-2003
Member Rating: 2.5


(1)
Message 125 of 785 (854862)
06-13-2019 4:50 PM
Reply to: Message 121 by Faith
06-13-2019 4:45 PM


quote:

Well, but aren't you just talking about observed differences, and how do you know those differences are the result of mutations rather than the result of sexual recombination producing a new set of alleles?

What makes you think that sexual recombination would produce new alleles. If it did why wouldn’t they count as mutations ? And why do you think that actually comparing the sequences doesn’t give all the information you need ?


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JonF
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Posts: 6174
Joined: 06-23-2003


Message 126 of 785 (854863)
06-13-2019 5:01 PM
Reply to: Message 121 by Faith
06-13-2019 4:45 PM


Well, but aren't you just talking about observed differences, and how do you know those differences are the result of mutations rather than the result of sexual recombination producing/selecting a new set of alleles?

Easier than pie.

All recombinations are identical to the corresponding sequence in one parent (or both). So we can comp the three genomes and detect the recombinations.

Some relatively small amount of the offspring's DNA will not appear in either parent. Those we label as mutations. The particular mutations do not exist anywh else. (It is poss it may exist somewhere else but that wouldn't be a copy of the offspring's DNA; it would have to arise independently.)

Edited by JonF, : No reason given.


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Faith 
Suspended Member (Idle past 712 days)
Posts: 35298
From: Nevada, USA
Joined: 10-06-2001


Message 127 of 785 (854865)
06-13-2019 5:03 PM
Reply to: Message 119 by PaulK
06-13-2019 4:27 PM


Well, I don't think those are mutations, you see.

Why not ? It’s explicitly about changes to the DNA sequence.

But wouldn't the substitution of one allele for another show the same kinds of differences?

I think they are normally occurring variations based on the sexual recombination of built-in alleles.

You don’t actually know what the graphs are showing, do you ?
They are showing the frequency of particular changes in the gene sequences. Eg “A <> G” represents the replacement of adenine with guanine or vice versa.

Yes, I'm more or less winging it, so I expect to have a better understanding if the discussion progresses, but those differences in the placement of chemicals must also be the case when one allele replaces another. If there were no differences in that sequence there would be no differences in the proteins the sequence makes and no difference in the traits the protein brings about.

Besides, this presentation of supposed mutations is just too organized for how mutations are normally described as random. Why should they occur in such a regular looking pattern at all if they really are random mistakes in replication? As I said before, this is revolutionary information, isn't it? It simply does not fit the definitions we usually encounter.

So in fact the pattern more reasonably reflects built in variation than mutations.

Edited by Faith, : No reason given.


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Taq
Member
Posts: 8523
Joined: 03-06-2009


(1)
Message 128 of 785 (854866)
06-13-2019 5:11 PM
Reply to: Message 127 by Faith
06-13-2019 5:03 PM


Faith writes:

But wouldn't the substitution of one allele for another show the same kinds of differences?

No. The child's DNA sequence doesn't match any of the 4 alleles carried by the parents.

Here is a simple example. Each parent has two alleles, and the child gets one allele from each parent:

Father:

AAAAAAAAAAA
AAATAAAAAAA

Mother:
AAAAAAAAAAA
AGAAAAAAAAA

Child:
AAAAAAAACAA
AAAAAAAAAAA

The child has two all A alleles, on from each parent. However, there was a C mutation that happened in one of those alleles. We know it is a mutation because none of the parents' alleles had that sequence. The child now has a new allele due to that mutation.

Are you now saying that mutations never happen? If so, that's just nuts.

Edited by Taq, : No reason given.

Edited by Taq, : No reason given.

Edited by Taq, : No reason given.


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Faith 
Suspended Member (Idle past 712 days)
Posts: 35298
From: Nevada, USA
Joined: 10-06-2001


Message 129 of 785 (854867)
06-13-2019 5:14 PM
Reply to: Message 126 by JonF
06-13-2019 5:01 PM


Can we back up for a basic genetics discussion?
What happens in the DNA when say a brown-eyed Bb father and a brown-eyed Bb mother produce children? The Mendelian formula is one BB, two Bb and one bb, right? How is this expressed in the DNA?

Is the parents' B on one strand and b on the other?

I'm sure there must be a different sequence of the four chemicals for a B versus a b, right?


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JonF
Member
Posts: 6174
Joined: 06-23-2003


Message 130 of 785 (854868)
06-13-2019 5:15 PM
Reply to: Message 127 by Faith
06-13-2019 5:03 PM


But wouldn't the substitution of one allele for another show the same kinds of differences?

No, no, no, no.

If your allele is the same as your father's allele that's recombination.

If your allele is the same as your mother's allele that's recombination.

If your allele is different from both parent's alleles that's mutation because that's the label we use for that situation.

There is no other place your allele could come from. There's no allele bank where your parents could get a special one.


This message is a reply to:
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Taq
Member
Posts: 8523
Joined: 03-06-2009


Message 131 of 785 (854869)
06-13-2019 5:17 PM
Reply to: Message 129 by Faith
06-13-2019 5:14 PM


Re: Can we back up for a basic genetics discussion?
Faith writes:

What happens in the DNA when say a brown-eyed Bb father and a brown-eyed Bb mother produce children? The Mendelian formula is one BB, two Bb and one bb, right? How is this expressed in the DNA?
Is the parents' B on one strand and b on the other?

What happens during the production of sperm and eggs is that the genome is split into two. Some sperm will have B and some sperm will have b. The same for eggs.

I'm sure there must be a different sequence of the four chemicals for a B versus a b, right?

Yes. There can also be new mutations that happen in either allele, making it different from the B and b alleles found in the parents.


This message is a reply to:
 Message 129 by Faith, posted 06-13-2019 5:14 PM Faith has replied

Replies to this message:
 Message 132 by Faith, posted 06-13-2019 5:20 PM Taq has replied

  
Faith 
Suspended Member (Idle past 712 days)
Posts: 35298
From: Nevada, USA
Joined: 10-06-2001


Message 132 of 785 (854870)
06-13-2019 5:20 PM
Reply to: Message 131 by Taq
06-13-2019 5:17 PM


Re: Can we back up for a basic genetics discussion?
Could we ignore the mutations issue until I get how the Bs and bs show up in the DNA?

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Percy
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Posts: 20818
From: New Hampshire
Joined: 12-23-2000
Member Rating: 2.5


Message 133 of 785 (854871)
06-13-2019 5:21 PM
Reply to: Message 105 by caffeine
06-13-2019 1:32 PM


I guess I don't see traditional breeding and mutation breeding as the same thing. The examples you mentioned of mutations in dogs and cattle have come up in previous discussions, and I wasn't forgetting them when I said that mutations play almost no role in breeding. Your sense that mutations have been responsible for more breeding results than we give credit for seems a quite a stretch to me, though I would of course concede in the face of evidence. But that populations of domestic breeds revert so quickly to wild forms once out in the wild (see, for example, When domesticated animals return to the wild) argues strongly, at least to me, against mutations playing any meaningful role in breeding.

The lack of mutations at any meaningful frequency in traditional breeding on human timescales is the driving force behind efforts at mutation breeding where the mutation rate is artificially accelerated.

--Percy


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 Message 105 by caffeine, posted 06-13-2019 1:32 PM caffeine has replied

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Faith 
Suspended Member (Idle past 712 days)
Posts: 35298
From: Nevada, USA
Joined: 10-06-2001


Message 134 of 785 (854872)
06-13-2019 5:25 PM
Reply to: Message 130 by JonF
06-13-2019 5:15 PM


No, no, no, no.
If your allele is the same as your father's allele that's recombination.
If your allele is the same as your mother's allele that's recombination.

But I've got an allele from each parent don't I? Two alleles, one from each. If I've got a b from my father and a b from my mother are these going to be identical sequences of DNA? (if they are how are they going to reflect the complementary pairs of chemicals?)

What if I've got a b from my father and a B from my mother? What will the DNA look llke?

Edited by Faith, : No reason given.

Edited by Faith, : No reason given.

Edited by Faith, : No reason given.

Edited by Faith, : No reason given.


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PaulK
Member
Posts: 17169
Joined: 01-10-2003
Member Rating: 2.5


Message 135 of 785 (854873)
06-13-2019 5:28 PM
Reply to: Message 127 by Faith
06-13-2019 5:03 PM


quote:

Yes, I'm more or less winging it, so I expect to have a better understanding if the discussion progresses

Spouting nonsense because you don’t know what you are talking about is not a good way to gain understanding.

quote:

but those differences in the placement of chemicals must also be the case when one allele replaces another

And that is showing no sign of gaining understanding. Yes, alleles differ in sequence. But if the sequence found in the child does not match the sequence for the gene in either parent, it has to be a mutation.

quote:

Besides, this presentation of supposed mutations is just too organized for how mutations are normally described as random

At the level of the chemicals some substitutions are more probable than others. That is what the graphs show. (Besides the fact that we are talking about probabilities because these changes are random). If you roll two dice some totals are more likely than others. It’s still random. And that isn’t even the randomness we’re really talking about when we call mutations random.

quote:

I said before, this is revolutionary information, isn't it? It simply does not fit the definitions we usually encounter.

No, it’s just a detail that you won’t know about if you just skim the surface - and you haven’t even got that far.

quote:

So in fact the pattern more reasonably reflects built in variation than mutations.

Are you literally suggesting that differences from the parent’s genes are most likely not differences from the parent’s genes ? Because differences from the parent’s genes are mutations.

Or perhaps what you are saying is better expressed as “mutations are built into the reproductive process”.


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